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<p>Dear Shenli and Paolo,</p>
<p><br>
</p>
<p>I changed a bit the input for PW and PH and it did not crash for me (only at the very end, for some reason). I used QE 6.4.1, 8 cores,
<span>ifort 15.0.2 20150121</span>.</p>
<p><br>
</p>
<p>The input and output files are here (available temporary):</p>
<p><a href="https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB" class="OWAAutoLink" id="LPlnk613256" previewremoved="true">https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB</a></p>
<p><br>
</p>
<p>For reference, I show here only the input files:</p>
<p></p>
<div>&control<br>
calculation='scf',<br>
restart_mode='from_scratch',<br>
prefix='LCO'<br>
pseudo_dir = '/scratch/timrov/q-e-qe-6.4.1/pseudo/',<br>
outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/'<br>
/<br>
&system<br>
ibrav = -5,<br>
celldm(1) = 10.1352,<br>
celldm(4) = 0.47876847,<br>
nat = 10,<br>
ntyp = 3,<br>
ecutwfc = 40.0<br>
ecutrho = 320.0<br>
occupations='fixed'<br>
lda_plus_u = .true.,<br>
lda_plus_u_kind = 0,<br>
U_projection_type = 'atomic',<br>
Hubbard_U(2) = 3.0<br>
/<br>
&electrons<br>
conv_thr = 1.d-14<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF<br>
Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF<br>
O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF<br>
ATOMIC_POSITIONS {crystal}<br>
O 0.312627155 0.750000000 0.187372845<br>
O 0.750000000 0.187372845 0.312627155<br>
O 0.187372845 0.312627155 0.750000000<br>
O 0.687372845 0.250000000 0.812627155<br>
O 0.812627155 0.687372845 0.250000000<br>
O 0.250000000 0.812627155 0.687372845<br>
Co 0.000000000 0.000000000 0.000000000<br>
Co 0.500000000 0.500000000 0.500000000<br>
La 0.250000000 0.250000000 0.250000000<br>
La 0.750000000 0.750000000 0.750000000<br>
K_POINTS {automatic}<br>
4 4 4 0 0 0</div>
<p></p>
<p><br>
</p>
<p></p>
<div>phonons of LCO at Gamma<br>
&inputph<br>
prefix = 'LCO',<br>
outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/',<br>
tr2_ph = 1.0d-14,<br>
epsil = .true.<br>
fildyn='LCO.dynG',<br>
/<br>
0.000000000000000 0.000000000000000 0.000000000000000</div>
<p></p>
<p><br>
</p>
<p><span>Shenli</span>: Could you try please to use exactly the same inputs as me with QE 6.4.1 and see what happens?</p>
<p><br>
</p>
<p>Paolo: I do not know what to say why you obtain NaN's... Do you use exactly the same input as Shenli?</p>
<p><br>
</p>
<p>Greetings,</p>
<p>Iurii<br>
</p>
<p><br>
</p>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher<br>
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<font size="3" face="'Times New Roman', Times, serif" color="808080"><font size="3" face="'Times New Roman', Times, serif" color="808080">Swiss Federal Institute of Technology Lausanne (EPFL<font color="808080"><font face="'Times New Roman', Times, serif">)</font></font></font><br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Paolo Giannozzi <p.giannozzi@gmail.com><br>
<b>Sent:</b> Wednesday, November 13, 2019 11:13:09 AM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>It doesn't segfaults for me but it produces NaN's. Note that:</div>
<div>- SCF convergence with fixed occupancies is very bad. I started from the charge density and wavefunctions obtained with smearing.</div>
<div>- outdir='rhomb_U3', between ' '</div>
<div>Paolo<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Nov 12, 2019 at 10:52 PM Shenli Zhang <<a href="mailto:shlzhang@uchicago.edu">shlzhang@uchicago.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div lang="EN-US">
<div class="gmail-m_-2060381739345997068WordSection1">
<p class="MsoNormal"><span style="font-size:11pt">Dear Iurii,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Thank you so much for your reply. The output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred” is not in the output file of ph.x, but is in the output file generated by the slurm system, which
is a job scheduler for the cluster I use. In the ph.x output, there is no error message, but the program just stopped in the line
</span><span style="font-size:11pt; color:black">“Calculating the dnsorth_cart matrix…” </span><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">I double checked the memory setting, it doesn’t seem to be the problem here. As I’ve increased the number of CPUs used to the point where I could actually run DFPT+U on an orthorhombic supercell of the same
system. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">And thanks for the advice on the parameter settings. I reduced the ecutrho/ecutwfc here in order to do a quick test. I tried the ultrasoft pseudopotentials, and the error still persists. And yes my system is
a nonmagnetic insulator and the scf calculation converged successfully. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">The reason I think this error is probably due to the unit cell shape is because I also created an orthorhombic supercell of the same system with the same parameter settings, and I could run the DFPT+U without
any problem.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Shenli<u></u><u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">-- <u></u><u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Shenli Zhang</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Postdoc</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Pritzker School of Molecular Engineering</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">The University of Chicago</span><span style="color:black"><u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11pt; color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><span style="font-size:11pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<div style="border-color:rgb(181,196,223) currentcolor currentcolor; border-style:solid none none; border-width:1pt medium medium; padding:3pt 0in 0in">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of Timrov Iurii <<a href="mailto:iurii.timrov@epfl.ch" target="_blank">iurii.timrov@epfl.ch</a>><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Date: </b>Tuesday, November 12, 2019 at 11:31 AM<br>
<b>To: </b>"<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Subject: </b>Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
</div>
<div id="gmail-m_-2060381739345997068divtagdefaultwrapper">
<p><span style="font-size:12pt; color:black">Dear </span><span style="color:black">Shenli Zhang</span><span style="font-size:12pt; color:black">,<u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="color:black">> with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred”</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="color:black">Was is printed in the output file of the PHonon calculation after the crash?
</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="color:black">Check if you have enough RAM to run DFPT+U, because it is heavy.</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="color:black">Your input for a PW SCF calculation has some problem:</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="color:black">- ecutrho/ecutwfc = 4 - this is true for norm-conserving pseudopotentials. But you are using PAW, for which the ratio should be 8 or more. Try to use DFPT+U with ultrasoft pseudopotentials (the ratio should be also 8 or more).</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="color:black">- nbnd=50 - this is not needed: just remove it from the input file</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="color:black">- occupations='fixed' : is your system a nonmagnetic insulator? Did your PW SCF calculation converged successfully?</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="color:black">- conv_thr=1.0d-12 : I suggest to try conv_thr=1.0d-14 if you plan to compute phonons afterwards.</span><span style="font-size:12pt; color:black"><u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="font-size:12pt; color:black">HTH<u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
<p><span style="font-size:12pt; color:black">Regards,<u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black">Iurii<u></u><u></u></span></p>
<p><span style="font-size:12pt; color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-family:Times; color:gray">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher</span><span style="color:black"><u></u><u></u></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:Times; color:gray">STI - IMX - THEOS and NCCR - MARVEL</span><span style="color:black"><u></u><u></u></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:Times; color:gray">Swiss Federal Institute of Technology Lausanne (EPFL)</span><span style="color:black"><u></u><u></u></span></p>
</div>
<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span style="font-family:Times; color:gray">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</span><span style="color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="http://people.epfl.ch/265334" target="_blank">http://people.epfl.ch/265334</a><u></u><u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:11pt; color:black">From:</span></b><span style="font-size:11pt; color:black"> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf
of Shenli Zhang <<a href="mailto:shlzhang@uchicago.edu" target="_blank">shlzhang@uchicago.edu</a>><br>
<b>Sent:</b> Tuesday, November 12, 2019 5:57:47 PM<br>
<b>To:</b> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<b>Subject:</b> [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)</span><span style="font-size:11pt">
<u></u><u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Dear all,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">I’m testing phonon calculations using ph.x with DFPT+U in QE 6.4 and QE 6.4.1, however the calculation always stops at the line “Calculating the dnsorth_cart matrix…” with an output error “forrtl:
severe (174): SIGSEGV, segmentation fault occurred”</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">I ran my system without U successfully. And I also ran the LiCoO2 +U example successfully. The only difference I can think of between my input file and the example file is the unit cell shape, where
my LaCoO3 system has a rhombohedral unit cell and the example LiCoO2 has an orthorhombic one. Could this be a problem or did I make some mistakes?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Attached are the input files for my system LCO. Thank you!</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">SCF calculation input:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&control</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> calculation='scf'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> prefix='LaCoO3p_relax'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> outdir=rhomb_U3</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> pseudo_dir = '/home/shlzhang/QE_simulation/LaCoO3/pseudo',</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&system</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> nbnd=50</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> ibrav=-5, celldm(1)=10.1352, celldm(4) =0.47876847, nat=10, ntyp= 3,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> ecutwfc =90, ecutrho =360, !for PAW ecutrho=4*ecutwfc, but need test</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> occupations='fixed' !energy units in Ry</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> lda_plus_u=.true. Hubbard_U(2)=3</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&electrons</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">conv_thr=1.0d-12</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&ions</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&cell</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">!cell_dofree='shape'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">ATOMIC_SPECIES</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">ATOMIC_POSITIONS (crystal)</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.312627155 0.750000000 0.187372845</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.750000000 0.187372845 0.312627155</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.187372845 0.312627155 0.750000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.687372845 0.250000000 0.812627155</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.812627155 0.687372845 0.250000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">O 0.250000000 0.812627155 0.687372845</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Co -0.000000000 0.000000000 -0.000000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Co 0.500000000 0.500000000 0.500000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">La 0.250000000 0.250000000 0.250000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">La 0.750000000 0.750000000 0.750000000</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">K_POINTS automatic</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> 4 4 4 0 0 0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Phonon calculation input:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">phonons of bulk LaCoO3 at Gamma</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">&inputph</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> prefix='LaCoO3p_relax'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> outdir=rhomb_U3</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> fildyn='LaCoO3.dyn'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> max_seconds=82800</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> tr2_ph=1.0d-14</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> verbosity='debug'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> amass(1)=138.9055</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> amass(2)=58.9332</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> amass(3)=16</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> epsil=.true.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black"> trans=.true.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">/</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">0.00000000000 0.000000000000 0.000000000000000 </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">-- </span><u></u><u></u></p>
<div>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Shenli Zhang</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Postdoc</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">Pritzker School of Molecular Engineering</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt; color:black">The University of Chicago</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11pt; color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><u></u><u></u></p>
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Phone +39-0432-558216, fax +39-0432-558222<br>
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